diff --git a/README.md b/README.md index e69de29..a5fe9bf 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,56 @@ +# ORFFinder +ORFFinder in Python. Inspired by NCBI's version: https://www.ncbi.nlm.nih.gov/orffinder/ + +### Installation: +`pip3 install orffinder` + +### Usage +Import the package + +```py +from Bio import SeqIO +import orffinder + +sequence = SeqIO.read("gene.fasta", "fasta") +orffinder.getORFs(sequence, minimum_length=75, remove_nested=True) +``` + +### Documentation +**getORFs()** +``` +Returns the loci of discovered ORFs in a dictionary format. + +sequence: sequence in Biopython Seq or String format. +minimum_length: minimum size of ORF in nucleotides. Default: 75 +start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"] +stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"] +remove_nested: remove all ORFs completely encased in another. Default: False +trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False +``` + +**getORFNucleotides()** +``` +Returns the loci of discovered ORFs in a dictionary format. + +sequence: sequence in Biopython Seq or String format. +return_loci: return the loci together with the nucleotide sequences. Default: False +minimum_length: minimum size of ORF in nucleotides. Default: 75 +start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"] +stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"] +remove_nested: remove all ORFs completely encased in another. Default: False +trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False +``` + +**getORFProteins()** +``` +Returns the loci of discovered ORFs in a dictionary format. + +sequence: sequence in Biopython Seq or String format. +translation_table: translation table as per BioPython. Default: 1 +return_loci: return the loci together with the protein sequences. Default: False +minimum_length: minimum size of ORF in nucleotides. Default: 75 +start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"] +stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"] +remove_nested: remove all ORFs completely encased in another. Default: False +trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False +``` diff --git a/orffinder/orffinder.py b/orffinder/orffinder.py index 375683f..61a3f44 100644 --- a/orffinder/orffinder.py +++ b/orffinder/orffinder.py @@ -149,8 +149,8 @@ def getORFNucleotides (sequence, return_loci=False, **kwargs): Returns the loci of discovered ORFs in a dictionary format. sequence: sequence in Biopython Seq or String format. - return_loci: return the loci together with the nucleotide sequences. - minimum_length: minimum size of ORF in nucleotides. + return_loci: return the loci together with the nucleotide sequences. Default: False + minimum_length: minimum size of ORF in nucleotides. Default: 75 start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"] stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"] remove_nested: remove all ORFs completely encased in another. Default: False @@ -191,8 +191,9 @@ def getORFProteins (sequence, translation_table=1, return_loci=False, **kwargs): Returns the loci of discovered ORFs in a dictionary format. sequence: sequence in Biopython Seq or String format. - return_loci: return the loci together with the protein sequences. - minimum_length: minimum size of ORF in nucleotides. + translation_table: translation table as per BioPython. Default: 1 + return_loci: return the loci together with the protein sequences. Default: False + minimum_length: minimum size of ORF in nucleotides. Default: 75 start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"] stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"] remove_nested: remove all ORFs completely encased in another. Default: False